Arxiu d'etiquetes: chromosomes

Sequencing the human genome

Genomics is a new science which has had a very important boom in recent years, thanks to advanced technologies of DNA sequencing, advances in bioinformatics and increasingly sophisticated techniques for analysing whole genomes. And I will discuss in this article about whole genomes and their sequencing, mentioning the Human Genome Project, which allowed the sequencing of the human genome.

WHY WE SEQUENCED?

Sequencing is the set of methods and biochemical techniques aimed at determining the order of nucleotides (A, T, C and G). Its objective is to get in order all nucleotides DNA of an organism.

The first organisms sequenced were two bacteria, Haemophilus influenzae and Mycoplasma genitalium in 1995. One year later, the genome of a fungus was sequenced (Saccharomyces cerevisiae).

From that moment comes the eukaryotic sequencing project: in 1998 Caenorhabditis elegans (nematode) was sequenced, in 2000 Drosophila melanogaster (fruit fly) and in 2001 the human genome.

But, why we sequenced? In the case of human genome, there is the need to know to help alleviate or prevent diseases.

Some of the organisms sequenced are model organisms, which have:

  • Medical importance: there are pathogens and we know diseases that they can cause.
  • Economic importance: organisms that humans eat, they can improve with the molecular techniques.
  • Study of evolution: in 2007 more than 11 species of Drosophila were sequenced and it tried to understand the evolutionary relationship between their chromosomes. It has also been made in mammals (ENCORE Project).

WHAT WE UNDERSTAND FOR GENOME SEQUENCED?

The human genome has 46 chromosomes, it means 23 chromosome pairs (22 autosomal chromosome pairs and 1 sexual chromosome pair, XX or XY depending if it is female or male).

The size of the human genome sequenced is 32,000Mb, 23 chromosomes plus Y chromosome.

The human genome was obtained from the mixture of human genomes to obtain a representation of all humanity genome.

PARADOX THAT WE FIND IN GENOME

A paradox is a statement that, despite apparently sound reasoning from true premises, leads to a self-contradictory or a logically unacceptable conclusion. In genomes we find two clear paradoxes.

The first one refers to the C-value, which represents the amount of DNA in the genome. As would be expected, if the organism is larger and more complex, the size of its genome will be bigger. However this is not true because there is not this correlation. It is due because the genome not only contains coding genome and proteins, but also contains repetitive DNA. In addition, the most compacted genomes are found in organisms less complexes.

The second paradox refers to the G-value, which represents the number of genes. There is no correlation between the number of genes and its complexity. A clear example is that in human genome has around 20,000 genes and Arabidopsis thaliana (herbaceous plant) has 25,000 genes. The reason is found in the RNA world, which is more complex and it is related to gene regulation.

THE HUMAN GENOME PROJECT (HGP)

The human genome sequencing project has been the most important biomedical research project of the whole history. With a budget of 3 thousand millions of dollars and the participation of an International Public Consortium, which was formed by EEUU, UK, Japan, France, Germany, China and other countries. Its ultimate objective was achieving the complete sequence of the human genome.

It started in 1990, but things get complicated when, in 1999, appeared a private company, Celera Genomics, headed by the scientist Craig J. Venter, who launched the challenge of getting the human sequence in record time, before the expected by the Public Consortium.

At the end it was decided to leave in a draw. The Public Consortium accelerated the process and obtained the draft almost at the same time. On 26th June 2000, in a ceremony at the White House with President Bill Clinton, the two leading representatives of the parties in competition, Craig Venter by Celera and the Public Consortium director, Francis Collins found. It announced the achievement of two drafts of the complete human genome sequence (Video 1). It was a historic moment, as the discovery of the double helix or the first time the man went to the Moon.

Video 1. Human Genome announcement at the White House (Source: YouTube)

The corresponding publications of both sequences did not appear until February 2001. The Public Consortium published its sequence in the journal Nature, while Celera did in Science (Figure 1). Three years later, in 2004, the Consortium published the final or complete version of the human genome.

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Figure 1. Covers publications of the human genome sequence draft in Nature and Science magazines in February 2001 (Source: Bioinformática UAB)

PERSONAL GENOMES

The genome of the year 2001 is the reference genome. From here we have entered in the era of personal genomes, with names and surnames. Craig Venter was the first person who sequenced his genome, and the next one was James Watson, one of the discoverers of double helix.

It took 13 years to sequence the reference genome. It took less time to sequence Craig Venter’s genome and only few months for Watson’s genome.

CLINICAL APPLICATIONS OF SEQUENCING

Without going to sequence the entire genome they have been identified disease-causing genes. An exome is not the whole genome, but the part of the genome corresponding to exons.

An example is the case of Nicholas Volker (Figure 2), the first case of genomic medicine. This child had a severe and intractable inflammatory bowel disease of unknown cause. With exome sequencing was allowed to discover a mutation in the XIAP gene on chromosome X, replacing an amino acid functionally important for another. A bone marrow transplant saved the life of the patient.

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Figure 2. Nicholas Volker with his book One in a Billion, which tells his story (Source: Rare & Undiagnosed Network)

REFERENCES

  • L. Pray. Eukaryotic genome complexity. Nature Education 2008; 1(1):96
  •  Brown. Genomes 3, 3rd edition (2007)
  • Bioinformática UAB
  • BT.com
  • E. A. Worthey et al. Making a definitive diagnosis: Successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease. Genetics in Medicine 2011; 13, 255-262
  • Main picture: Noticias InterBusca

MireiaRamos-angles

Why I look similar to my parents?

The reason of the similitude with our parents is genetics. This science studies the inheritance; it means how offspring resemble their parents, the diseases that are transmitted from generation to generation… It is biology’s discipline growing quickly and it affects biology, healthy and society in general. In this article I am going to talk about what is genetics and the DNA’s discovery.

HOW GENETIC INFORMATION IS INHERITED?

The genetic information is inherited to the offspring by genes, which are the storage unit of this information. They are located inside the chromosomes and they occupy specific positions. The number of chromosomes is constant inside species, but different between other species.

In humans the number of chromosomes is 46. In each cell we have 46 chromosomes, which 44 are autosomal, i.e., not a chromosome sexual and 2 chromosomes sexual. The total of 46 chromosomes is the human genome.

Our genome consist of 2 sets of 23 chromosomes counterparts. This means that each set have the same characteristics respect the other set and one comes from our mother by ovum and the other one comes from our father by sperm (Figure 1). Inherit each set of our progenitor is the reason why we resemble they, but also is via that we inherit some genetic diseases.

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Figure 1. Human female karyotype, i.e., the graphical representation of chromosomes. They are placed in pairs sorted and size, from the largest to the pair smaller, plus the sex chromosomes (Source: Mireia Ramos, Cerba Internacional SAE)

CHEMISTRY OF GENES

Genes are parts of DNA (deoxyribonucleic acid), comprising by the join of small molecules that called nucleotide. These nucleotides contain a pentose (compound of 5 carbon), a phosphate and a nucleobase (organic compound with an atom of nitrogen) (Figure 2). There are 4 nucleobase: two purines (adenine and guanine) and two pyrimidines (thymine and cytosine). These nucleobases distinguish each nucleotide and their arrangement constitutes the genetic code.

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Figure 2. Details of the chemistry of DNA (Source: Eduredes: Los ácidos nucleicos)

But all knowledge about DNA and genes is recent. The structure of DNA was discovered by James Watson and Francis Crick in 1953 in Cambridge (Figure 3). Previously, other scientists had done studies to try to determine the similarity between relatives, but it was not until this discovery it was understood that there was chemistry behind it.

Figure 3. Francis Crick (right) and James Watson (left) with the construction of the structure of DNA (Source: The DNA store)

THE BEGINNING OF THEIR STORY

Watson, an American 23 year-old biologist, and Crick, an English 35 year-old physicist, worked in the Cavendish Laboratory in Cambridge. They spent many months building models of molecules and comparing them to the information they had, but still they couldn’t find the correct structure of DNA.

In the King’s College of London, the physicist Maurice Wilkins and Rosalind Franklin, another physicist with knowledge in crystallography. She took X-ray pictures of DNA (Figure 4).

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Figure 4. The four people who contributed to the discovery of DNA (Source: Biology: The people responsible for the discovery of DNA)

Watson and Crick, after present a wrong model of the triple helix, told Maurice Wilkins about what they were trying to do and he showed them a new and better X-ray picture of DNA, which had been taken by Rosalind Franklin, without her permission. This was the picture number 51 to help them solve the mystery (Figure 5).

photo 51 explanation
Figure 5. Explanation of picture 51 that used Watson and Crick (Source: Seguramente estaré equivocado: La “fotografía 51”)

When the university’s Cavendish Laboratory was still at its old site at nearby Free School Lane, the pub was a popular lunch destination for staff working there. Thus, it became the place where Francis Crick interrupted patrons’ lunchtime on 28th February 1953 to announce that he and James Watson had “discovered the secret of life” after they had come up with their proposal for the structure of DNA. This day is called for someone the 8th day of Creation.

The 25th April 1953 it published their article with 900 words in Nature (Figure 6). Three years earlier had published law Chargaff, which was one of the foundations to apply the theory of the double helix of DNA. This law establishes the complementarity of the bases in DNA, i.e., adenine (A) pairs with thymine (T) and the same with guanine (G) and cytosine (C) (Figure 2). So the amount of purine (A and G) is equal to the amount of the pyrimidine (T and C).

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Figure 6. Article published in the journal Nature, which shows the picture 51 (Source: The DNA store)

THE IMPORTANCE OF GENETICS

It has been argued that the discovery of DNA as well as our understanding of its structure and function may well be the most important discovery of the last century. The effect of the discovery of DNA on scientific and medical progress has been enormous, whether it involves the identification of the genes that trigger major diseases or the creation and manufacture of drugs to treat these devastating diseases. In fact, the identification of these genes and their subsequent analysis in terms of therapeutic treatment has ultimately influenced science and will continue to do so in the future.

While the discovery of DNA has been a significant one in the twentieth century, it will continue to revolutionize medicine, agriculture, forensics, paternity and many other important fields in society today. DNA research encompasses an evolving area of progress and continued funding and interest in its relevance will likely fuel new discoveries in the future.

REFERENCES

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